Contacts of the helix formed by residues 37 - 48 (chain C) in PDB entry 1LXF
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 37 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C CYS 4.2 1.3 + - - -
36C ILE* 1.3 77.7 - - - +
38C THR* 1.3 59.6 + - - +
39C LYS* 3.1 19.7 + - - +
40C GLU* 3.3 15.0 + - - +
41C LEU* 2.8 30.0 + - - +
61C ILE* 4.1 11.4 - - - -
70C GLY 4.6 3.1 - - - -
71C THR* 3.7 16.8 - - - +
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Residues in contact with THR 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C SER* 1.3 76.3 - - - +
39C LYS* 1.3 64.8 + - - +
41C LEU* 4.0 6.3 - - - -
42C GLY* 3.6 1.4 + - - -
54C PRO* 4.3 19.2 + - - +
57C LEU* 3.0 42.3 - - - +
58C GLN* 3.3 47.6 - - + +
61C ILE* 4.6 8.1 - - + -
70C GLY 5.4 2.7 - - - +
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Residues in contact with LYS 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C SER* 3.1 9.3 + - - +
38C THR* 1.3 84.4 + - - +
40C GLU* 1.3 65.6 + - + +
42C GLY* 3.8 1.6 + - - -
43C LYS* 3.6 23.9 + - - +
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Residues in contact with GLU 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ILE 2.9 17.2 - - - +
27C PHE 2.6 33.5 - - - +
28C VAL* 4.7 2.5 - - - -
29C LEU* 3.9 7.1 - - - +
30C GLY* 3.7 26.0 + - - +
31C ALA* 5.2 5.4 - - + +
35C CYS 5.3 2.2 - - - +
36C ILE* 3.9 9.4 - - + -
37C SER* 3.3 17.4 + - - +
39C LYS* 1.3 77.7 - - + +
41C LEU* 1.3 64.1 + - - +
43C LYS* 2.6 42.9 + - - +
44C VAL* 3.3 4.8 + - - +
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Residues in contact with LEU 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C PHE* 3.8 21.1 - - + -
36C ILE* 3.4 20.6 - - + -
37C SER 2.8 16.7 + - - +
38C THR* 3.9 2.5 - - - +
40C GLU* 1.3 74.6 - - - +
42C GLY* 1.3 57.7 + - - +
43C LYS 2.6 12.1 + - - -
44C VAL* 2.6 15.1 + - - -
45C MET* 3.0 29.8 + - + -
57C LEU* 3.5 26.0 - - + -
60C MET* 4.9 1.3 - - + -
61C ILE* 3.9 5.2 - - + -
92C BEP 2.9 52.5 - - + -
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Residues in contact with GLY 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C THR 3.6 2.2 + - - -
39C LYS 3.8 2.9 + - - -
40C GLU 3.4 0.6 - - - -
41C LEU* 1.3 78.1 - - - +
43C LYS* 1.3 61.5 + - - +
45C MET* 3.8 8.0 - - - +
46C ARG* 2.9 27.7 + - - +
50C GLN 4.7 0.3 - - - +
52C PRO* 4.6 7.9 - - - +
57C LEU* 3.0 23.8 - - - +
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Residues in contact with LYS 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ILE* 5.9 0.2 - - - -
29C LEU* 4.3 19.3 - - + -
39C LYS* 3.6 16.5 + - - +
40C GLU* 2.6 42.2 + - - +
41C LEU 2.6 4.4 + - - -
42C GLY* 1.3 72.9 - - - +
44C VAL* 1.3 63.8 + - + +
46C ARG* 3.5 7.4 - - - +
47C MET* 3.4 23.3 + - + +
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Residues in contact with VAL 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ALA* 5.6 0.4 - - + -
26C ILE* 3.6 16.6 - - + +
27C PHE* 2.9 79.4 - - + +
40C GLU 4.1 2.2 - - - +
41C LEU 2.6 7.8 + - - +
43C LYS* 1.3 69.7 - - - +
45C MET* 1.3 57.4 + - - +
47C MET* 2.5 31.1 + - - -
48C LEU* 2.6 38.0 - - + +
92C BEP 4.8 0.2 - - + -
153I MET* 4.3 2.0 - - - -
156I ALA* 4.3 7.6 - - + -
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Residues in contact with MET 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LEU* 3.0 26.1 + - + +
42C GLY 3.8 4.5 - - - +
44C VAL* 1.3 77.1 - - - +
46C ARG* 1.3 57.0 + - - +
48C LEU* 2.5 29.4 + - + +
49C GLY 3.1 0.2 + - - -
50C GLN* 2.7 53.8 + - + +
52C PRO* 3.6 30.1 - - + -
57C LEU* 4.6 0.4 - - + -
60C MET* 4.4 20.4 - - + -
92C BEP 3.4 38.4 - - + +
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Residues in contact with ARG 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C GLY 2.9 19.5 + - - +
43C LYS* 3.5 8.3 - - - +
44C VAL 3.0 0.2 + - - -
45C MET* 1.3 75.2 - - - +
47C MET* 1.3 61.6 + - + +
48C LEU 3.4 0.3 + - - -
49C GLY* 3.6 9.4 + - - -
50C GLN 2.7 11.4 + - - +
51C ASN* 3.0 31.4 + - + +
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Residues in contact with MET 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ILE* 3.2 35.9 - - + -
29C LEU* 5.6 2.0 - - + -
43C LYS* 3.5 15.5 - - + +
44C VAL 2.5 16.2 + - - +
46C ARG* 1.3 76.2 - - + +
48C LEU* 1.3 56.0 + - - -
49C GLY 3.4 2.4 + - - -
155I GLN* 3.6 22.0 - - - +
156I ALA* 3.3 30.8 + - + +
160I ALA* 5.8 6.1 - - + -
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Residues in contact with LEU 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C VAL* 2.6 45.0 + - + +
45C MET* 2.5 25.4 + - + +
47C MET* 1.3 76.8 - - - +
49C GLY* 1.3 58.2 + - - -
50C GLN* 3.3 6.8 - - + +
92C BEP 3.0 45.1 - - + -
152I ALA* 3.2 34.6 - - + +
153I MET* 3.5 19.7 - - - +
155I GLN* 4.9 3.4 - - - +
156I ALA* 3.4 13.2 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il